Advanced Photon SourceBldg. 401/Rm A4113Argonne National Laboratory9700 S. Cass Ave.Argonne, IL 60439 USAwww.aps.anl.govapsinfo@aps.anl.gov

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How the Advanced Photon Sourceat

Argonne National LaboratoryPowers the Fight Against Disease

DisclaimerThis report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agencythereof, nor UChicago Argonne, LLC, nor any of their employees or officers, makes any warranty, express or implied, or assumes any legal liability or responsibility forthe accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately ownedrights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constituteor imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of document authors expressedherein do not necessarily state or reflect those of the United States Government or any agency thereof, Argonne National Laboratory, or UChicago Argonne, LLC.

A BRIGHT LIGHT FOR

DRUG DISCOVERY

Fast Facts about the APSScientific disciplines investigated at the APS: Pharmaceutical research; materials and chemical sci-

ence; environmental, geological, and planetary science;physics; polymer science; biological and life science; atomic,molecular, and optical physics; and the properties ofnanoscale materials.

Some benefits accruing from research at the APS: Clues to the causes of and treatments for a multitude of

diseases including AIDS, and toxic threats such as anthrax. Better materials for lithium-ion batteries and other en-

ergy-related technologies.The path to more efficient designs for fuel-injection sys-

tems. A greater understanding of human physiology. Ways of eliminating and remediating environmental

depredations. Insights about conditions at the center of the Earth, the

causes of earthquakes and volcanoes, and the compositionof cosmic dust.

A nearly endless array of new information about materi-als that support the development of practical applicationssuch as advanced digital storage media, more efficient light-ing, environmentally friendly refrigerants, methods for in-creasing the durability of man-made structures, and thecharacterization of nanostructures whose sizes are meas-ured in atoms, to name but a few.

The APS facility:Electrons cannot go faster than the speed of light, but

getting them close to it produces some amazing effects, oneof which is length contraction: The electrons in the APS stor-age ring have an energy of 7 billion electron volts), so theyare traveling at over 99.99999999% the speed of light.

There are over 2000 conventional electromagnets and 16pulsed electromagnets in the APS electron accelerators.

Over 700 beam-position monitors, 600 corrector mag-nets, and 80 computer systems monitor and correct theelectron orbit, steering x-ray beams to within a fraction ofthe width of a human hair.

More than 120 programmable logic controllers monitor-ing over 25,000 signals comprise radiation interlock systemsprotecting personnel and equipment.

The APS has five 1-megawatt radio frequency (rf) powersystems (the equivalent of 5000 microwave ovens) that areused to accelerate and maintain high-energy electronbeams in the storage ring.

The storage ring rf systems contribute to a combined ac-celerating voltage equal to a 16-million-volt power supply.

APS rf systems produce more rf power than the com-bined output of every radio and television station in the cityof Chicago.

The superconducting detectors that collect data from theinteraction of high-brightness APS x-rays and the samplebeing studied operate at temperatures colder than outerspace.

The outer diameter of the APS experiment hall is 1225feet; slightly less than the height of the Willis (Sears) Towerin Chicago (1454 feet).

Experiment hall construction required 56,000 cubic yardsof concrete (equal to a football-field-sized block 30 feethigh); 5000 tons of structural steel (enough for 3500 mid-size cars); 2,000,000 linear feet (380 miles) of electricalwire; and 190,000 feet of pipe for water, steam, drainage,and HVAC.

Total floor space of all APS buildings is 1,042,811 feet2.Facility construction started in spring 1990; research

started in the fall of 1996.Total APS construction and project cost at completion in

1995 was $812 million (1995 dollars).The number of APS employees is approximately 450.

Photo of Venkatraman Ramakrishnan ©2014 the Nobel Foundation; photo of Ada Yonath ©2014 American Committee for the Weizmann Institute of Science; photo ofThomas Steitz ©2014 Yale University; photo of Robert Lefkowitz ©2014 Duke University. Aerial photography by Tigerhill Studio, http://www.tigerhillstudio.com/.All other photographs: Argonne National Laboratory

For more information about the APS, please contact Dr. Stephen Streiffer, Argonne Associate Laboratory Director forPhoton Sciences and Director, Advanced Photon Source • aps-director@anl.gov • (630) 252-7990

On the front cover: Advanced Photon Source user Prof. Brian Kobilka (Stanford University) preparing a protein crystalfor study in one of the x-ray beamlines operated by the National Institute of General Medical Sciences and National Can-cer Institute structural biology facility at the Advanced Photon Source. Kobilka and his colleague Prof. Robert Lefkowitz(Duke University) were awarded the 2012 Nobel Prize in Chemistry for research largely carried out at this facility.

The Advanced Photon Source and

Today’s Pharmaceuticals, and Tomorrow’sDevelopment of many critically important phar-

maceuticals, existing and yet to come, grows out ofmacromolecular x-ray crystallography (MX)-basedresearch carried out at sources of high-brightnessx-rays such as the U.S. Department of Energy (DOE)Office of Science’s Advanced Photon Source (APS)at Argonne National Laboratory and the APS Up-grade (APS-U), which will open new vistas in drugdiscovery.

MX is a research technique that reveals, to atomicresolution, the structure of macromolecules (pro-teins, protein and protein DNA complexes, and virusparticles) in a crystal. The crystalline arrangement ofmolecules causes a beam of x-rays to diffract intomany specific directions, which can be analyzed todetermine structure. This technique has been at theforefront of the symbiotic relationship betweensources of high-brightness x-rays such as the APS anddrug discovery.

Approximately 30% of therapeutically relevantprotein targets are routinely studied at the APS; theremaining 70% do not benefit from extensive struc-tural guidance because the crystals are too small ordiffract too poorly with current x-ray capabilities.

The Advanced Photon Source FacilityThe high-energy, high-brightness, highly-penetrat-

ing x-rays from the APS give researchers access to apowerful, versatile light that is ideal for studying thearrangements of molecules and atoms, probing theinterfaces where materials meet, watching chemicalprocesses that happen on the nanoscale, and deter-mining the interdependent form and function of bi-ological proteins.

The APS facility — which is large enough to encir-cle a major-league baseball stadium — includes par-ticle accelerators that produce, accelerate, and storea beam of high-energy (relativistic) electrons. As theelectrons orbit through powerful electromagnets,they are deflected by permanent-magnet devicesand emit synchrotron radiation, which covers abroad segment of the electromagnetic spectrumwith wavelengths that are shorter than visible light.These wavelengths are invisible to the human eyeand include extreme ultraviolet and x-ray radiation.They match the corresponding features of atoms,molecules, crystals, and cells — just as the longerwavelengths of visible light match the sizes of thesmallest things the human eye can see.

Structure and function are intimately related. X-ray crystallography is the most comprehensive techniqueavailable to determine the structure of any molecule at atomic resolution. Accurate knowledge of molecularstructures is a prerequisite for rational drug design and structure-based functional studies. Results from x-ray crystallographic studies provide unambiguous, accurate, and reliable 3-dimensional structural parametersat times even before complete chemical characterization is available. In addition, crystallography is the onlymethod for determining the “absolute” configuration of a molecule.

Jeffrey R. Deschamps, “The Role of Crystallography in Drug Design”

Access to Beam Time at the APSAll beam time at the APS (either non-proprietary or proprietary) can be requested each cycle through the web-based

Beam Time Access System. A proposal describes an experiment and identifies the experimental team. A beam time requeston a proposal identifies where and when the researchers want beam time. A proposal can have several beam time re-quests. For information and inquiries about accessing beam time at the APS, contact Dr. Dennis Mills, Argonne DeputyAssociate Laboratory Director for X-ray Science • dmm@aps.anl.gov • (630) 252-5680

Sector 14: BioCARS-CATSector 14: BioCARS-CAT

Sector 17: IMCA-CATSector 17: IMCA-CAT Sector 19: SBC-CATSector 19: SBC-CAT

Sector 21: LS-CATSector 21: LS-CAT

Sector 22: SER-CATSector 22: SER-CAT

Sector 23: GM/CA-XSDSector 23: GM/CA-XSD

Sector 24: NE-CATSector 24: NE-CAT

Sector 31: LRL-CATSector 31: LRL-CAT

The APS facility at Argonne National Laboratory. Sectors comprise one or more x-ray beamlines. Locations of themacromolecular x-ray crystallography sectors (see facing page) are indicated in the photo above.

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Ribosome G-protein-coupled receptor

Macromolecular x-ray crystallography has alwaysbeen a major initiative for users of the APS.

• MX beamlines at the APS are highly automated,efficient, and productive.

• Of the 68 APS x-ray beamlines currently in op-eration, 16, or nearly one-quarter, are dedicatedto MX.

• In fiscal year (FY) 2017, 1774 of 5742 APS users(31%) were biology or life sciences researchers(the majority of those carried out MX studies),making them the largest of the APS researchcommunities.

• In FY 2017, MX researchers at the APS published33% of the facility’s peer-reviewed journal articles

• MX researchers using the APS have determinedover 20,000 protein structures, more than at anyother x-ray light source — nearly as many as allother U.S. light sources combined, and 20% of allstructures from light sources worldwide1.

MX beamlines at the APS are independently fundedand operated, and they continually invest in capitalequipment and other upgrades to maintain state-of-the-art capabilities for some of the most challengingproblems in structural biology.

These beamlines are at the forefront of MX re-search techniques. Microbeam crystallography tech-nology is an evolving research tool, and time-resolvedcrystallography, serial crystallography, and solutionscattering are potential growth areas.

All three recipients of the 2009 Nobel Prize in Chem-istry, Professors Venkatraman Ramakrishnan (Cam-bridge Medical Research Center), Thomas Steitz (YaleUniversity), and Ada Yonath (Weizmann Institute) pub-lished papers on their award-winning work based ondata collected at the Structural Biology Center Collab-orative Access Team (SBC-CAT) MX facility at the APS,and other DOE light sources. They shared the award fortheir study of the structure and function of the ribo-some (below left), which works as a protein factory inall organisms from humans to bacteria, and is the targetof many antibiotics.

The 2012 Nobel Prize in Chemistry, awarded to Pro-fesssors Brian Kobilka (Stanford University) and RobertLefkowitz (Howard Hughes Medical Institute and DukeUniversity) for their work on G-protein-coupled recep-tors (GPCRs), was supported in large part by researchperformed by Kobilka at the National Institute of Gen-eral Medical Sciences and National Cancer Institutestructural biology facility (GM/CA-XSD) at the APS. Thiswork determined the first structure of a human GPCR(below right), which are responsible for a number of bi-ological responses, and are the target for 40% of allpharmaceuticals.

The following pages highlight some of today’s drugs thatemerged from research at the APS, a few examples of in-vestigations that could produce tomorrow’s breakthroughs,and an introduction to an upgraded APS that promises evengreater success in supporting drug development.1http://bit.ly/2yioV7M

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The pharmaceutical industry has a history of usingMX to enable pre-clinical drug-discovery research atstorage ring x-ray light sources like the APS. Now, theAPS is on the brink of a transformational advance: themulti-bend achromat (MBA) arrangement of compo-nents in a light source electron accelerator.

This is the centerpiece of the APS Upgrade (APS-U),which will reconfigure the APS electron storage ring(a rendering of one upgraded sector is shown at right),driving orders-of- magnitude increases in x-ray bright-ness and the number of photons that illuminate asample being studied. The APS-U will provide high-in-tensity, high-energy x-rays that can be focused tosub-micron sizes to maximize the amount of data col-lected from a single crystal. The APS-U will revolution-ize MX research by allowing thousands of potentialdrug-target structures to be determined in a singleday. These vast improvements in photon beam prop-erties, combined with rapid, ongoing advances inx-ray instrumentation, computing, and theory willmake it possible for researchers at the upgraded APSto explore a new landscape of scientific problems thatpreviously were completely inaccessible, includingthose related to MX, which is widely recognized as themost powerful tool to determine structure at theatomic level and, as noted on page 1, “a prerequisite

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Simulated x-ray beam source profiles, comparing the beam from the APS today (left) to thebeam from an upgraded APS storage ring (right), which will exceed the capabilities of today’shard x-ray storage rings by 2 to 3 orders of magnitude in brightness and coherent flux. Nar-rowing the APS x-ray beam to a spot as opposed to a “pancake” will deliver more photons tothe sample being studied, which will greatly increase the amount of information obtained andthe speed at which that information is collected.

for rational drug design and structure-based func-tional studies.”

The APS Upgrade, with its greatly expandedthroughut of excellent crystallographic data, promisesto drive explosive growth in structure-guided drug dis-covery and transform the pharmaceutical industry’ssearch for and optimization of new and improveddrugs for the all-important fight against disease.

Drug Discovery and the APS Upgrade

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Kaletra®, one of the most successful drugs used tostop the progression of the human immunodeficiencyvirus (HIV) into AIDS, got its start at the APS when scien-tists from Abbott Laboratories used the Industrial Macro-molecular Crystallography Association CollaborativeAccess Team (IMCA-CAT) x-ray beamline at the APS todiscover a way to stop HIV from replicating in the bodythrough the use of a protease inhibitor that blocks thebreakdown of proteins.

They pinpointed how the atoms of Kaletra® interactwith the viral protein and where the drug should targetthe virus.

The drug was designed to fit into a hole in the HIV pro-tease protein, lock into position there, and prevent HIVfrom replicating.

Out of that work came the drug Kaletra®.In 2002, Kaletra® became the most prescribed drug in

its class for AIDS therapy, and it remains widely usedtoday, prolonging the lives of thousands of AIDS patients.

A Drug That FightsAIDS

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Kaletra®

To help design the drug Zelboraf®, which can halt the progres-sion of malignant and inoperable skin cancer, researchers fromPlexxikon, Inc., and Genentech, the drug discovery and manufac-turing companies, respectively, that developed the melanomatreatment, used the x-ray light sources at three DOE national lab-oratories—SLAC National Accelerator Laboratory, Lawrence Berke-ley National Laboratory, and the Structural Biology Center (SBC)CAT x-ray beamlines at the Argonne APS.

Zelboraf® is the first drug to treat advanced melanoma by tar-geting a specific gene mutation.

Zelboraf® was extremely successful during clinical trials in dis-rupting the disease and extending the lives of those who were di-agnosed with it.

A Drug That FightsSkin Cancer

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Early research that led to the development of Januvia®,a type 2 diabetes medication manufactured by Merck &Co., was done on the IMCA-CAT beamline at the APS.Januvia® helps lower blood sugar levels in adults withtype 2 diabetes, and Januvia® is the top-selling brand inits class.

The drug was approved by the U.S. Food and Drug Ad-ministration (FDA) in 2006 and is one of the most populartype 2 diabetes drugs on the market. In 2007, the FDAapproved a variation of Januvia® called Janumet®, whichis a combination of sitagliptin and metformin, and is alsomade by Merck.

Type 2 diabetes, once known as adult-onset or non-in-sulin-dependent diabetes, is a chronic condition that af-fects the way the body metabolizes sugar (glucose). Thebody either resists the effects of insulin — a hormonethat regulates the movement of sugar into cells — ordoesn't produce enough insulin to maintain a normal glu-cose level.

More common in adults, type 2 diabetes increasinglyaffects children as childhood obesity increases. There isno cure.

A Drug That FightsType 2 Diabetes

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Januvia®

The research that led to the development of Votrient®,a successful drug for fighting advanced kidney cancer, wascarried out by scientists from GlaxoSmithKline using theIMCA-CAT x-ray beamline at the APS.

The American Cancer Society’s most recent estimatesfor kidney cancer in the United States in 2017 noted63,990 new cases of kidney cancer (40,610 in men and23,380 in women), with about 14,400 fatalities (9470 menand 4930 women) from this disease. These numbers in-clude all types of kidney and renal pelvis cancers.

Votrient® is an angiogenesis inhibitor, which interfereswith the growth of new blood vessels needed for solid can-cer tumors to survive.

Votrient® is used to treat advanced renal cell carcinoma(kidney cancer). Votrient® is also used to treat soft tissuesarcoma, a tumor that can develop in or around muscles,tendons, joints, organs, or blood vessels.

A Drug That FightsKidney Cancer

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Votrient®

Venetoclax™, from AbbVie, a small-molecule drug that treatschronic lymphocytic leukemia in those with a specific chromosomalabnormality, emerged from research at the IMCA-CAT x-ray beamlineat the APS. The researchers studied the structure of a particular pro-tein and how it interacted with potential inhibitors.

In April 2016, Venclexta™ was approved by the FDA to treatchronic lymphocytic leukemia (CLL), one of the most common typesof leukemia in adults with about 15,000 cases diagnosed each year.10% to 20% of patients with CLL have a chromosomal abnormalityin which a portion of the chromosome that inhibits cancer growthis missing.

Patients with that abnormality comprise 30% to 50% of relapsesafter CLL treatment and often have a life expectancy of two to threeyears.

Venclexta™ is the first FDA-approved treatment that targets a pro-tein that blocks programmed cell death and can promote the growthof CLL cells.

A Drug That FightsLeukemia

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Macromolecular x-ray crystallography data collected at theSoutheast Regional (SER) CAT beamlines at the APS were employedto investigate the development of VRC01, extraordinary antibodiesthat can neutralize about 90% of all strains of HIV. An understand-ing of how VRC01 antibodies are generated might ultimately leadto the ability to induce similar antibodies in HIV-infected people.

The researchers examined the crystal structures of several anti-bodies from the VRC01 lineage and identified significant differ-ences in their amino acid sequences. They also tracked thedevelopment of the VRC01 B cell lineage and found that it involvedhundreds of generations of B cells that evolve faster than HIV-1(the predominant strain of the virus), allowing the development ofVRC01 antibodies that can neutralize the virus effectively. However,during natural HIV infection, VRC01 does not develop into its ma-ture form quickly enough to protect people from the virus.

The results of this study, therefore, have important implicationsin the development of a long-awaited HIV vaccine.

Closer to an EffectiveHIV Vaccine

Crystal structures (insets) of several diverse antibodies from the VRC01lineage. Ribbon representations highlight the third complementarity deter-mining regions (red) and disulfides (green).

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A new therapeutic opportunity for modified retinals that helps improvevision, and offers a major improvement over current therapeutics designedto perturb cell signaling in the eye, was aided by research at a Northeast-ern (NE) CAT x-ray beamline at the APS.

A light-sensing pigment found in everything from bacteria to vertebratescan be biochemically manipulated to reset itself, an important therapeuticadvantage.

Researchers used a modified form of vitamin A, called “locked retinal,”to induce the recycling mechanism and engage proteins central to humanvision.

The targeted proteins include light-sensing rhodopsin, which belongs tothe family of proteins — GPCRs — that sit in cell membranes and transmitexternal cellular cues into internal cell signaling pathways.

Comparison of two rhodopsin binding pockets based on x-ray diffraction data ob-tained at NE-CAT at the APS. From S. Gulati et al., Proc. Natl. Acad. Sci. USA114(13), E2608 (Published online March 13, 2017). © 2017 National Academy ofSciences.

A Therapy forImproved Vision

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A Key Target forCancer Drugs

The structure of the EGFR protein.

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Many approved cancer therapies target a protein called “epidermal growthfactor receptor” (EGFR) that regulates many crucial cellular processes and —when mutated — can promote the proliferation of tumor cells. Scientists, carryingout research at a GM/CA-XSD x-ray beamline at the APS, made a fundamentaldiscovery about EGFR signaling that may open the potential for new types of can-cer drugs.

Science has long known that growth factors activate EGFR by “stitching” tworeceptor molecules together. This paradigm has always suggested that the re-ceptor has to be either “off” or “on,” so all EGFR drugs have been designed toshut off the receptor and thus shut off proliferation. But a longstanding puzzlewas that the EGFR is regulated by a total of seven growth factors, which can makethe cell take different actions. How can those different actions be driven by a sin-gle binding (and activation) scenario?

The researchers found that EGFR signaling is not just an on/off process con-trolled by stitching two receptors together. Rather, the growth factors can turnon the receptor in a spectrum of different ways, depending on the strength ofthe stitch and the timing of this binding. Instead of therapeutics that just shutoff EGFR, new ones might be designed that encourage it to give a beneficial sig-nal.

The spectrum of effects from different EGFR binding mechanisms also mighthelp shed light on other biological mysteries such as the causes of liver cancer,where pathways that work in similar ways to EGFR signaling play major roles thathave not been well explained.

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Science has been work-ing for decades to im-prove upon the firstnon-steroidal anti-inflam-matory drug (NSAID),commonly known as as-pirin. Newer versions ofNSAIDs such as ibuprofen,naproxen, and celecoxibare the mainstay of treat-ment for pain, from minorbumps and bruises tomore serious chronic painand inflammatory condi-tions such as arthritis andcancer, but these drugsalso have gastrointestinalside effects and are associated with rare fatal adverse reactions.

Researchers utilized the Lilly Research Laboratories (LRL) CAT x-ray beamline atthe APS to study the structure of the microsomal prostaglandin synthase 1 (mPGES-1 enzyme) with the aim of providing a framework for the rational design of new mol-ecules that can control inflammation and pain without troublesome side effects.

Their approach was to selectively inhibit an enzyme that generates a specific in-flammatory lipid compound without blocking other lipids that are important in theregulation of blood clotting, blood pressure, and control of gastrointestinal integrity,thus eliminating the associated side effects that those lipids control.

These findings offer an opportunity for optimizing the interaction between the in-hibitors and mPGES-1 to improve the action of potential drugs.

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Representation of the mPGES-1 active site with an inhibitorshown in a yellow stick model and glutathione shown in a ma-genta stick model. Two of the three mPGES monomers thatform the active site are shown in cyan and orange.

Cancer, aging, and a host of other diseases are linked to damage or “lesions”in DNA, the molecular blueprint for a cell. The body has developed a sophis-ticated machinery to deal with DNA damage. For example, a certain humantranslesion polymerase can bypass DNA damage caused by ultraviolet radia-tion.

The polymerase can also bypass intentional damage inflicted by the anti-cancer drug cisplatin, leading to chemoresistance.

Sometimes the polymerase can get it wrong, leading to errors in the repli-cated DNA. Damage that takes the form of a segment of DNA bound to thecancer-causing chemical 1,N6-ethenodeoxyadenosine (“etheno”) triggerserror-prone bypass by polymerase.

To learn why the polymerase makes miscoded DNA in this case, researcherssolved the structure of polymerase in complex with etheno-damaged DNAusing x-ray data collected at the Life Sciences (LS) CAT x-ray facility at the APS.Their insights into how polymerases bypass DNA damage may pave the wayto the discovery of inhibitors of translesion synthesis, helping chemothera-peautics such as cisplatin remain effective.

BypassingDNA Damage

Structural basis of error-prone bypass of the etheno-dA DNA adduct by human poly-merase revealed by the crystal structure of the ternary polymerase•DNA•dNTP complextrapped at the insertion stage.

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Scientists utilized the high-brightness x-rays from the APS at a SBC-CAT x-ray beamline to detail the structure of a molecule, TREM2, thathas been implicated in Alzheimer’s disease.

TREM2 also has been implicated in other inflammatory conditions,including chronic obstructive pulmonary disease and stroke, making thestructure of TREM2 important for understanding chronic and degener-ative diseases throughout the body.

Knowing the shape of the molecule — and how that shape may bedisrupted by certain genetic mutations — can help in understandinghow Alzheimer’s and the other neurodegenerative diseases developand how to prevent and treat them.

The Molecular Roots ofAlzheimer’s Disease

The structure of TREM2.

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Research at a BioCARS-CAT x-ray beamline at the APS showed thatsmall modifications to the anti-viral drug pleconaril may make it an ef-fective treatment against modern versions of enterovirus D68, whichcauses a severe respiratory disease.

Most enteroviruses are stabilized by a molecule that occupies a bind-ing pocket found in the protective shell of the virus. When the virusbinds to a human cell, this molecule is squeezed out of its pocket,destabilizing the virus. The virus then disintegrates and releases its ge-netic material into the cell, where it replicates and, ultimately, causesinfection.

Researchers used the APS to determine the crystal structure of EV-D68 by itself and when bound to the anti-viral drug pleconaril, whichthey discovered was effective against the 1962 strain of the virus.

Comparing the crystal structures with and without pleconaril indi-cated that the drug displaces a fatty acid contained within the hy-drophobic pocket of the 1962 strain. The results may suggest potentialalterations to the drug to make it effective against current strains ofthe virus.

Treatments forRespiratory Disease

This color-coded image shows the surface view of enterovirus D68. The virushas stricken children with serious respiratory infections and might be associ-ated with polio-like symptoms. Red regions are the highest peaks, and thelowest portions are blue. In the black-and-white background are actual elec-tron microscopy images of the EV-D68 virus. Image: Yue Liu and Michael G.Rossmann (Purdue University)

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• Bacterial cell survival depends on the integrity of its genetic information and the stabilityof replicated chromosomes during cell division. Bacteria that package genomic DNA aslinear chromosomes face a special challenge: their ends are prone to damage from DNAdegradation or aberrant repair reactions. The ends of the chromosomes fold into tighthairpins that protect the DNA while permitting accurate replication of genetic materialat the chromosome ends. Research at BioCARS-CAT produced a clearer understandingof the process, which is important for the development of protelomerase inhibitors thatmay be useful in treating certain bacterial infections.

• Data collected at GM/CA-XSD showed how receptor-binding site (RBS)-directed antibod-ies bind to the viral protein hemagglutinin (HA) — the key target of antibodies that pro-tect against the influenza virus, revealing important implications for understanding themechanisms involved in the binding of RBS-directed antibodies with HA, as well as theirapplication to the development of improved vaccine design.

• Studies at IMCA-CAT elucidating the interactions of enzymes that are central to ubiqui-tination (the addition of ubiquitin to a substrate target protein) are critical to under-standing how the complex ubiquitin system works and to the rational design of drugsthat target an ever-widening array of ubiquitin-related diseases.

• Researchers working at LRL-CAT have created the first atomic-level structural models ofthe protein Rumi in complex with a major signaling protein called Notch, which controlsthe expression of genes that help determine which cells should develop into specific celltypes like skin, heart, or neurons. These models reveal the details of Rumi’s interactionswith Notch, paving the way for potential anti-cancer medications that target Rumi.

• Researchers using LS-CAT revealed the inner workings of the hepatitis C virus (HCV) RNAreplication, and the way in which sofosbuvir (brand name Sovaldi®), a remarkably effec-tive drug against HCV, interacts with an active site on HCV, potentially providing an av-enue for the rational design of additional therapeutics against HCV.

• The structure of the human serotonin transporter in complex with serotonin-specific re-uptake inhibitors, determined at NE-CAT, provides important new information about howantidepressants block serotonin binding and transporter activity, the possible role ofknown disease mutations, and allosteric regulation of the transporter, thus aiding in thedesign of small molecules capable of more-precise activity against a variety of neuro-logical disorders.

• Research conducted at SER-CAT solved the structure of an enzyme (the laforin glucanphosphatase) responsible for the formation of insoluble glucan inclusion bodies thatcause neuronal death, thus providing important insights into both the basis of Laforadisease and normal glycogen metabolism.

• Molecular x-ray crystallography experiments at SBC-CAT determined the first three-di-mensional structure of the two-pore channel (TPC) voltage-gated ion channel protein ina closed conformation, providing an avenue for treatments that target TCPs in lysosomaldiseases and Ebola.

Today’s Research forTomorrow’s Pharmaceuticals

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Sector 14: BioCARS-CAT is mainly supported by the National Institute of General Medical Sciences (NIGMS)of the National Institutes of Health (NIH) and is dedicated to the development of resources and facilities tofoster frontier research in time-resolved macromolecular x-ray crystallography and time-resolved biologicalsmall-angle and wide-angle scattering. Watching macromolecules in action furthers our understanding of howmacromolecules function, ultimately leading to advances in the cause, prevention, and treatment of diseases.

Sector 17 (beamline 17-ID): IMCA-CAT, dedicated to accelerating drug discovery research, operates a state-of-the-art structural biology synchrotron beamline for the pharmaceutical industry. The facility is optimizedfor high-quality, high-throughput macromolecular crystallography experiments, producing essential data fordetermining the structures of key components in structure-based drug design. The facility is funded by thepharmaceutical members of IMCA (Industrial Macromolecular Crystallography Association): AbbVie, Bristol-Myers Squibb, Merck, Novartis, and Pfizer, and operated through a contract with the Hauptman-WoodwardMedical Research Institute. Data from IMCA-CAT have been crucial to the development of a significant numberof therapeutics for the prevention and treatment of disease.

Sector 19: SBC-CAT, which is funded by the DOE Office of Biological and Environmental Research, operates anational user facility for macromolecular x-ray crystallography at the APS in order to advance and promotescientific and technological innovation in support of the DOE mission by providing world-class scientific re-search and advancing scientific knowledge. SBC-CAT is an important component of integrated biosciencesand contributes to the expansion of existing programs and exploration of new opportunities in structural bi-ology, proteomics, and genomics research with a major focus on medicine, bio-nanomachines, and biocatalysisthat are highly relevant to health, energy resources, a clean environment, and national security.

Sector 21: LS-CAT, which is supported by the Michigan Economic Development Corporation and the MichiganTechnology Tri-Corridor, provides macromolecular x-ray crystallography resources for those with a need todetermine the structure of proteins via access to state-of-the-art x-ray diffraction facilities.

Sector 22: SER-CAT, which is operated by the University of Georgia and funded by supporting institutions(www.ser-cat.org/members.html), provides third-generation x-ray capabilities to macromolecular x-ray crys-tallographers and structural biologists in the southeastern region of the U.S. Emphasis is placed on structuredetermination, high-resolution structural analyses, large unit cells, drug design, structural genomics, soft x-ray data collection, and next-generation beamline automation.

Sector 23: GM/CA-XSD, which is located organizationally within the APS, operates a user facility for structuralbiology with synchrotron beamlines specializing in intense, tunable micro-beams for crystallography to de-termine the structure of proteins and other macromolecules at the forefront of biological research, with anemphasis on problems in structural genomics and structure-based drug design. The scientific and technicalgoals of GM/CA-XSD emphasize streamlined, efficient throughput for a variety of sample types, sizes, andqualities representing the cutting edge of structural biology research. GM/CA-XSD is funded in whole or inpart with federal funds from the National Cancer Institute and NIGMS of the NIH.

Sector 24: NE-CAT is managed by Cornell University for its seven member institutions (http://necat.chem.cornell.edu/aboutus/Organization/Members.htm). NE-CAT, which is supported primarily by a grant fromNIGMS of the NIH with additional financial support from the member institutions, operates an x-ray crystal-lographic research facility designed to address the most demanding and complex diffraction problems in struc-tural biology and is organized to allow its operation to be driven by the requirements of its users.

Sector 31: LRL-CAT, which is operated by Eli Lilly and Company, is dedicated to the determination of proteinstructures and the analysis of the interactions between potential pharmaceutical compounds and a proteinof interest to further research into the causes, prevention, and treatment of disease.

MX Sectors at the APS

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For more information about the APS, please contact Dr. Stephen Streiffer, Argonne Associate Laboratory Director forPhoton Sciences and Director, Advanced Photon Source • aps-director@anl.gov • (630) 252-7990

On the front cover: Advanced Photon Source user Prof. Brian Kobilka (Stanford University) preparing a protein crystalfor study in one of the x-ray beamlines operated by the National Institute of General Medical Sciences and National Can-cer Institute structural biology facility at the Advanced Photon Source. Kobilka and his colleague Prof. Robert Lefkowitz(Duke University) were awarded the 2012 Nobel Prize in Chemistry for research largely carried out at this facility.

The Advanced Photon Source and

Today’s Pharmaceuticals, and Tomorrow’sDevelopment of many critically important phar-

maceuticals, existing and yet to come, grows out ofmacromolecular x-ray crystallography (MX)-basedresearch carried out at sources of high-brightnessx-rays such as the U.S. Department of Energy (DOE)Office of Science’s Advanced Photon Source (APS)at Argonne National Laboratory and the APS Up-grade (APS-U), which will open new vistas in drugdiscovery.

MX is a research technique that reveals, to atomicresolution, the structure of macromolecules (pro-teins, protein and protein DNA complexes, and virusparticles) in a crystal. The crystalline arrangement ofmolecules causes a beam of x-rays to diffract intomany specific directions, which can be analyzed todetermine structure. This technique has been at theforefront of the symbiotic relationship betweensources of high-brightness x-rays such as the APS anddrug discovery.

Approximately 30% of therapeutically relevantprotein targets are routinely studied at the APS; theremaining 70% do not benefit from extensive struc-tural guidance because the crystals are too small ordiffract too poorly with current x-ray capabilities.

The Advanced Photon Source FacilityThe high-energy, high-brightness, highly-penetrat-

ing x-rays from the APS give researchers access to apowerful, versatile light that is ideal for studying thearrangements of molecules and atoms, probing theinterfaces where materials meet, watching chemicalprocesses that happen on the nanoscale, and deter-mining the interdependent form and function of bi-ological proteins.

The APS facility — which is large enough to encir-cle a major-league baseball stadium — includes par-ticle accelerators that produce, accelerate, and storea beam of high-energy (relativistic) electrons. As theelectrons orbit through powerful electromagnets,they are deflected by permanent-magnet devicesand emit synchrotron radiation, which covers abroad segment of the electromagnetic spectrumwith wavelengths that are shorter than visible light.These wavelengths are invisible to the human eyeand include extreme ultraviolet and x-ray radiation.They match the corresponding features of atoms,molecules, crystals, and cells — just as the longerwavelengths of visible light match the sizes of thesmallest things the human eye can see.

Structure and function are intimately related. X-ray crystallography is the most comprehensive techniqueavailable to determine the structure of any molecule at atomic resolution. Accurate knowledge of molecularstructures is a prerequisite for rational drug design and structure-based functional studies. Results from x-ray crystallographic studies provide unambiguous, accurate, and reliable 3-dimensional structural parametersat times even before complete chemical characterization is available. In addition, crystallography is the onlymethod for determining the “absolute” configuration of a molecule.

Jeffrey R. Deschamps, “The Role of Crystallography in Drug Design”

Access to Beam Time at the APSAll beam time at the APS (either non-proprietary or proprietary) can be requested each cycle through the web-based

Beam Time Access System. A proposal describes an experiment and identifies the experimental team. A beam time requeston a proposal identifies where and when the researchers want beam time. A proposal can have several beam time re-quests. For information and inquiries about accessing beam time at the APS, contact Dr. Dennis Mills, Argonne DeputyAssociate Laboratory Director for X-ray Science • dmm@aps.anl.gov • (630) 252-5680

Sector 14: BioCARS-CATSector 14: BioCARS-CAT

Sector 17: IMCA-CATSector 17: IMCA-CAT Sector 19: SBC-CATSector 19: SBC-CAT

Sector 21: LS-CATSector 21: LS-CAT

Sector 22: SER-CATSector 22: SER-CAT

Sector 23: GM/CA-XSDSector 23: GM/CA-XSD

Sector 24: NE-CATSector 24: NE-CAT

Sector 31: LRL-CATSector 31: LRL-CAT

The APS facility at Argonne National Laboratory. Sectors comprise one or more x-ray beamlines. Locations of themacromolecular x-ray crystallography sectors (see facing page) are indicated in the photo above.

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Advanced Photon SourceBldg. 401/Rm A4113Argonne National Laboratory9700 S. Cass Ave.Argonne, IL 60439 USAwww.aps.anl.govapsinfo@aps.anl.gov

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Argonne National LaboratoryPowers the Fight Against Disease

DisclaimerThis report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agencythereof, nor UChicago Argonne, LLC, nor any of their employees or officers, makes any warranty, express or implied, or assumes any legal liability or responsibility forthe accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately ownedrights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constituteor imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of document authors expressedherein do not necessarily state or reflect those of the United States Government or any agency thereof, Argonne National Laboratory, or UChicago Argonne, LLC.

A BRIGHT LIGHT FOR

DRUG DISCOVERY

Fast Facts about the APSScientific disciplines investigated at the APS: Pharmaceutical research; materials and chemical sci-

ence; environmental, geological, and planetary science;physics; polymer science; biological and life science; atomic,molecular, and optical physics; and the properties ofnanoscale materials.

Some benefits accruing from research at the APS: Clues to the causes of and treatments for a multitude of

diseases including AIDS, and toxic threats such as anthrax. Better materials for lithium-ion batteries and other en-

ergy-related technologies.The path to more efficient designs for fuel-injection sys-

tems. A greater understanding of human physiology. Ways of eliminating and remediating environmental

depredations. Insights about conditions at the center of the Earth, the

causes of earthquakes and volcanoes, and the compositionof cosmic dust.

A nearly endless array of new information about materi-als that support the development of practical applicationssuch as advanced digital storage media, more efficient light-ing, environmentally friendly refrigerants, methods for in-creasing the durability of man-made structures, and thecharacterization of nanostructures whose sizes are meas-ured in atoms, to name but a few.

The APS facility:Electrons cannot go faster than the speed of light, but

getting them close to it produces some amazing effects, oneof which is length contraction: The electrons in the APS stor-age ring have an energy of 7 billion electron volts), so theyare traveling at over 99.99999999% the speed of light.

There are over 2000 conventional electromagnets and 16pulsed electromagnets in the APS electron accelerators.

Over 700 beam-position monitors, 600 corrector mag-nets, and 80 computer systems monitor and correct theelectron orbit, steering x-ray beams to within a fraction ofthe width of a human hair.

More than 120 programmable logic controllers monitor-ing over 25,000 signals comprise radiation interlock systemsprotecting personnel and equipment.

The APS has five 1-megawatt radio frequency (rf) powersystems (the equivalent of 5000 microwave ovens) that areused to accelerate and maintain high-energy electronbeams in the storage ring.

The storage ring rf systems contribute to a combined ac-celerating voltage equal to a 16-million-volt power supply.

APS rf systems produce more rf power than the com-bined output of every radio and television station in the cityof Chicago.

The superconducting detectors that collect data from theinteraction of high-brightness APS x-rays and the samplebeing studied operate at temperatures colder than outerspace.

The outer diameter of the APS experiment hall is 1225feet; slightly less than the height of the Willis (Sears) Towerin Chicago (1454 feet).

Experiment hall construction required 56,000 cubic yardsof concrete (equal to a football-field-sized block 30 feethigh); 5000 tons of structural steel (enough for 3500 mid-size cars); 2,000,000 linear feet (380 miles) of electricalwire; and 190,000 feet of pipe for water, steam, drainage,and HVAC.

Total floor space of all APS buildings is 1,042,811 feet2.Facility construction started in spring 1990; research

started in the fall of 1996.Total APS construction and project cost at completion in

1995 was $812 million (1995 dollars).The number of APS employees is approximately 450.

Photo of Venkatraman Ramakrishnan ©2014 the Nobel Foundation; photo of Ada Yonath ©2014 American Committee for the Weizmann Institute of Science; photo ofThomas Steitz ©2014 Yale University; photo of Robert Lefkowitz ©2014 Duke University. Aerial photography by Tigerhill Studio, http://www.tigerhillstudio.com/.All other photographs: Argonne National Laboratory